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224,200 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | get_indelcaller | def get_indelcaller(d_or_c):
"""Retrieve string for indelcaller to use, or empty string if not specified.
"""
config = d_or_c if isinstance(d_or_c, dict) and "config" in d_or_c else d_or_c
indelcaller = config["algorithm"].get("indelcaller", "")
if not indelcaller:
indelcaller = ""
if is... | python | def get_indelcaller(d_or_c):
"""Retrieve string for indelcaller to use, or empty string if not specified.
"""
config = d_or_c if isinstance(d_or_c, dict) and "config" in d_or_c else d_or_c
indelcaller = config["algorithm"].get("indelcaller", "")
if not indelcaller:
indelcaller = ""
if is... | [
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224,201 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | split_snps_indels | def split_snps_indels(orig_file, ref_file, config):
"""Split a variant call file into SNPs and INDELs for processing.
"""
base, ext = utils.splitext_plus(orig_file)
snp_file = "{base}-snp{ext}".format(base=base, ext=ext)
indel_file = "{base}-indel{ext}".format(base=base, ext=ext)
for out_file, s... | python | def split_snps_indels(orig_file, ref_file, config):
"""Split a variant call file into SNPs and INDELs for processing.
"""
base, ext = utils.splitext_plus(orig_file)
snp_file = "{base}-snp{ext}".format(base=base, ext=ext)
indel_file = "{base}-indel{ext}".format(base=base, ext=ext)
for out_file, s... | [
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224,202 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | get_samples | def get_samples(in_file):
"""Retrieve samples present in a VCF file
"""
with utils.open_gzipsafe(in_file) as in_handle:
for line in in_handle:
if line.startswith("#CHROM"):
parts = line.strip().split("\t")
return parts[9:]
raise ValueError("Did not fin... | python | def get_samples(in_file):
"""Retrieve samples present in a VCF file
"""
with utils.open_gzipsafe(in_file) as in_handle:
for line in in_handle:
if line.startswith("#CHROM"):
parts = line.strip().split("\t")
return parts[9:]
raise ValueError("Did not fin... | [
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224,203 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | _get_exclude_samples | def _get_exclude_samples(in_file, to_exclude):
"""Identify samples in the exclusion list which are actually in the VCF.
"""
include, exclude = [], []
to_exclude = set(to_exclude)
for s in get_samples(in_file):
if s in to_exclude:
exclude.append(s)
else:
includ... | python | def _get_exclude_samples(in_file, to_exclude):
"""Identify samples in the exclusion list which are actually in the VCF.
"""
include, exclude = [], []
to_exclude = set(to_exclude)
for s in get_samples(in_file):
if s in to_exclude:
exclude.append(s)
else:
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224,204 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | exclude_samples | def exclude_samples(in_file, out_file, to_exclude, ref_file, config, filters=None):
"""Exclude specific samples from an input VCF file.
"""
include, exclude = _get_exclude_samples(in_file, to_exclude)
# can use the input sample, all exclusions already gone
if len(exclude) == 0:
out_file = in... | python | def exclude_samples(in_file, out_file, to_exclude, ref_file, config, filters=None):
"""Exclude specific samples from an input VCF file.
"""
include, exclude = _get_exclude_samples(in_file, to_exclude)
# can use the input sample, all exclusions already gone
if len(exclude) == 0:
out_file = in... | [
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224,205 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | select_sample | def select_sample(in_file, sample, out_file, config, filters=None):
"""Select a single sample from the supplied multisample VCF file.
"""
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
if len(get_samples(in_file)) == 1:
shutil.... | python | def select_sample(in_file, sample, out_file, config, filters=None):
"""Select a single sample from the supplied multisample VCF file.
"""
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
if len(get_samples(in_file)) == 1:
shutil.... | [
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224,206 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | merge_variant_files | def merge_variant_files(orig_files, out_file, ref_file, config, region=None):
"""Combine multiple VCF files with different samples into a single output file.
Uses bcftools merge on bgzipped input files, handling both tricky merge and
concatenation of files. Does not correctly handle files with the same
... | python | def merge_variant_files(orig_files, out_file, ref_file, config, region=None):
"""Combine multiple VCF files with different samples into a single output file.
Uses bcftools merge on bgzipped input files, handling both tricky merge and
concatenation of files. Does not correctly handle files with the same
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224,207 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | _do_merge | def _do_merge(orig_files, out_file, config, region):
"""Do the actual work of merging with bcftools merge.
"""
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
_check_samples_nodups(orig_files)
prep_files = run_multicore(p_bgzip_and_... | python | def _do_merge(orig_files, out_file, config, region):
"""Do the actual work of merging with bcftools merge.
"""
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
_check_samples_nodups(orig_files)
prep_files = run_multicore(p_bgzip_and_... | [
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224,208 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | _check_samples_nodups | def _check_samples_nodups(fnames):
"""Ensure a set of input VCFs do not have duplicate samples.
"""
counts = defaultdict(int)
for f in fnames:
for s in get_samples(f):
counts[s] += 1
duplicates = [s for s, c in counts.items() if c > 1]
if duplicates:
raise ValueError(... | python | def _check_samples_nodups(fnames):
"""Ensure a set of input VCFs do not have duplicate samples.
"""
counts = defaultdict(int)
for f in fnames:
for s in get_samples(f):
counts[s] += 1
duplicates = [s for s, c in counts.items() if c > 1]
if duplicates:
raise ValueError(... | [
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224,209 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | _sort_by_region | def _sort_by_region(fnames, regions, ref_file, config):
"""Sort a set of regionally split files by region for ordered output.
"""
contig_order = {}
for i, sq in enumerate(ref.file_contigs(ref_file, config)):
contig_order[sq.name] = i
sitems = []
assert len(regions) == len(fnames), (regio... | python | def _sort_by_region(fnames, regions, ref_file, config):
"""Sort a set of regionally split files by region for ordered output.
"""
contig_order = {}
for i, sq in enumerate(ref.file_contigs(ref_file, config)):
contig_order[sq.name] = i
sitems = []
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224,210 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | concat_variant_files | def concat_variant_files(orig_files, out_file, regions, ref_file, config):
"""Concatenate multiple variant files from regions into a single output file.
Uses GATK4's GatherVcfs, falling back to bcftools concat --naive if it fails.
These both only combine samples and avoid parsing, allowing scaling to large... | python | def concat_variant_files(orig_files, out_file, regions, ref_file, config):
"""Concatenate multiple variant files from regions into a single output file.
Uses GATK4's GatherVcfs, falling back to bcftools concat --naive if it fails.
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224,211 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | _run_concat_variant_files_gatk4 | def _run_concat_variant_files_gatk4(input_file_list, out_file, config):
"""Use GATK4 GatherVcfs for concatenation of scattered VCFs.
"""
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
params = ["-T", "GatherVcfs", "-I", input_file_list, "-O", ... | python | def _run_concat_variant_files_gatk4(input_file_list, out_file, config):
"""Use GATK4 GatherVcfs for concatenation of scattered VCFs.
"""
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
params = ["-T", "GatherVcfs", "-I", input_file_list, "-O", ... | [
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224,212 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | _get_file_list | def _get_file_list(orig_files, out_file, regions, ref_file, config):
"""Create file with region sorted list of non-empty VCFs for concatenating.
"""
sorted_files = _sort_by_region(orig_files, regions, ref_file, config)
exist_files = [(c, x) for c, x in sorted_files if os.path.exists(x) and vcf_has_varia... | python | def _get_file_list(orig_files, out_file, regions, ref_file, config):
"""Create file with region sorted list of non-empty VCFs for concatenating.
"""
sorted_files = _sort_by_region(orig_files, regions, ref_file, config)
exist_files = [(c, x) for c, x in sorted_files if os.path.exists(x) and vcf_has_varia... | [
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224,213 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | _fix_gatk_header | def _fix_gatk_header(exist_files, out_file, config):
"""Ensure consistent headers for VCF concatenation.
Fixes problems for genomes that start with chrM by reheadering the first file.
These files do haploid variant calling which lack the PID phasing key/value
pair in FORMAT, so initial chrM samples cau... | python | def _fix_gatk_header(exist_files, out_file, config):
"""Ensure consistent headers for VCF concatenation.
Fixes problems for genomes that start with chrM by reheadering the first file.
These files do haploid variant calling which lack the PID phasing key/value
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Fixes problems for genomes that start with chrM by reheadering the first file.
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due to the lack of header... | [
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224,214 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | _run_concat_variant_files_bcftools | def _run_concat_variant_files_bcftools(in_list, out_file, config, naive=False):
"""Concatenate variant files using bcftools concat, potentially using the fast naive option.
"""
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
bcftools = config_u... | python | def _run_concat_variant_files_bcftools(in_list, out_file, config, naive=False):
"""Concatenate variant files using bcftools concat, potentially using the fast naive option.
"""
if not utils.file_exists(out_file):
with file_transaction(config, out_file) as tx_out_file:
bcftools = config_u... | [
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224,215 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | combine_variant_files | def combine_variant_files(orig_files, out_file, ref_file, config,
quiet_out=True, region=None):
"""Combine VCF files from the same sample into a single output file.
Handles cases where we split files into SNPs/Indels for processing then
need to merge back into a final file.
""... | python | def combine_variant_files(orig_files, out_file, ref_file, config,
quiet_out=True, region=None):
"""Combine VCF files from the same sample into a single output file.
Handles cases where we split files into SNPs/Indels for processing then
need to merge back into a final file.
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224,216 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | sort_by_ref | def sort_by_ref(vcf_file, data):
"""Sort a VCF file by genome reference and position, adding contig information.
"""
out_file = "%s-prep.vcf.gz" % utils.splitext_plus(vcf_file)[0]
if not utils.file_uptodate(out_file, vcf_file):
with file_transaction(data, out_file) as tx_out_file:
he... | python | def sort_by_ref(vcf_file, data):
"""Sort a VCF file by genome reference and position, adding contig information.
"""
out_file = "%s-prep.vcf.gz" % utils.splitext_plus(vcf_file)[0]
if not utils.file_uptodate(out_file, vcf_file):
with file_transaction(data, out_file) as tx_out_file:
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224,217 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | add_contig_to_header | def add_contig_to_header(line, ref_file):
"""Streaming target to add contigs to a VCF file header.
"""
if line.startswith("##fileformat=VCF"):
out = [line]
for region in ref.file_contigs(ref_file):
out.append("##contig=<ID=%s,length=%s>" % (region.name, region.size))
retu... | python | def add_contig_to_header(line, ref_file):
"""Streaming target to add contigs to a VCF file header.
"""
if line.startswith("##fileformat=VCF"):
out = [line]
for region in ref.file_contigs(ref_file):
out.append("##contig=<ID=%s,length=%s>" % (region.name, region.size))
retu... | [
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224,218 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | parallel_combine_variants | def parallel_combine_variants(orig_files, out_file, ref_file, config, run_parallel):
"""Combine variants in parallel by chromosome, concatenating final outputs.
"""
file_key = "vcf_files"
def split_by_region(data):
base, ext = utils.splitext_plus(os.path.basename(out_file))
args = []
... | python | def parallel_combine_variants(orig_files, out_file, ref_file, config, run_parallel):
"""Combine variants in parallel by chromosome, concatenating final outputs.
"""
file_key = "vcf_files"
def split_by_region(data):
base, ext = utils.splitext_plus(os.path.basename(out_file))
args = []
... | [
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224,219 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | move_vcf | def move_vcf(orig_file, new_file):
"""Move a VCF file with associated index.
"""
for ext in ["", ".idx", ".tbi"]:
to_move = orig_file + ext
if os.path.exists(to_move):
shutil.move(to_move, new_file + ext) | python | def move_vcf(orig_file, new_file):
"""Move a VCF file with associated index.
"""
for ext in ["", ".idx", ".tbi"]:
to_move = orig_file + ext
if os.path.exists(to_move):
shutil.move(to_move, new_file + ext) | [
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224,220 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | bgzip_and_index | def bgzip_and_index(in_file, config=None, remove_orig=True, prep_cmd="", tabix_args=None, out_dir=None):
"""bgzip and tabix index an input file, handling VCF and BED.
"""
if config is None:
config = {}
out_file = in_file if in_file.endswith(".gz") else in_file + ".gz"
if out_dir:
rem... | python | def bgzip_and_index(in_file, config=None, remove_orig=True, prep_cmd="", tabix_args=None, out_dir=None):
"""bgzip and tabix index an input file, handling VCF and BED.
"""
if config is None:
config = {}
out_file = in_file if in_file.endswith(".gz") else in_file + ".gz"
if out_dir:
rem... | [
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224,221 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | tabix_index | def tabix_index(in_file, config, preset=None, tabix_args=None):
"""Index a file using tabix.
"""
in_file = os.path.abspath(in_file)
out_file = in_file + ".tbi"
if not utils.file_exists(out_file) or not utils.file_uptodate(out_file, in_file):
# Remove old index files to prevent linking into t... | python | def tabix_index(in_file, config, preset=None, tabix_args=None):
"""Index a file using tabix.
"""
in_file = os.path.abspath(in_file)
out_file = in_file + ".tbi"
if not utils.file_exists(out_file) or not utils.file_uptodate(out_file, in_file):
# Remove old index files to prevent linking into t... | [
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224,222 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | is_gvcf_file | def is_gvcf_file(in_file):
"""Check if an input file is raw gVCF
"""
to_check = 100
n = 0
with utils.open_gzipsafe(in_file) as in_handle:
for line in in_handle:
if not line.startswith("##"):
if n > to_check:
break
n += 1
... | python | def is_gvcf_file(in_file):
"""Check if an input file is raw gVCF
"""
to_check = 100
n = 0
with utils.open_gzipsafe(in_file) as in_handle:
for line in in_handle:
if not line.startswith("##"):
if n > to_check:
break
n += 1
... | [
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224,223 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | cyvcf_add_filter | def cyvcf_add_filter(rec, name):
"""Add a FILTER value to a cyvcf2 record
"""
if rec.FILTER:
filters = rec.FILTER.split(";")
else:
filters = []
if name not in filters:
filters.append(name)
rec.FILTER = filters
return rec | python | def cyvcf_add_filter(rec, name):
"""Add a FILTER value to a cyvcf2 record
"""
if rec.FILTER:
filters = rec.FILTER.split(";")
else:
filters = []
if name not in filters:
filters.append(name)
rec.FILTER = filters
return rec | [
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224,224 | bcbio/bcbio-nextgen | bcbio/variation/vcfutils.py | cyvcf_remove_filter | def cyvcf_remove_filter(rec, name):
"""Remove filter with the given name from a cyvcf2 record
"""
if rec.FILTER:
filters = rec.FILTER.split(";")
else:
filters = []
new_filters = [x for x in filters if not str(x) == name]
if len(new_filters) == 0:
new_filters = ["PASS"]
... | python | def cyvcf_remove_filter(rec, name):
"""Remove filter with the given name from a cyvcf2 record
"""
if rec.FILTER:
filters = rec.FILTER.split(";")
else:
filters = []
new_filters = [x for x in filters if not str(x) == name]
if len(new_filters) == 0:
new_filters = ["PASS"]
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224,225 | bcbio/bcbio-nextgen | bcbio/pipeline/alignment.py | organize_noalign | def organize_noalign(data):
"""CWL target to skip alignment and organize input data.
"""
data = utils.to_single_data(data[0])
work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "align", dd.get_sample_name(data)))
work_bam = os.path.join(work_dir, "%s-input.bam" % dd.get_sample_name(da... | python | def organize_noalign(data):
"""CWL target to skip alignment and organize input data.
"""
data = utils.to_single_data(data[0])
work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "align", dd.get_sample_name(data)))
work_bam = os.path.join(work_dir, "%s-input.bam" % dd.get_sample_name(da... | [
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224,226 | bcbio/bcbio-nextgen | bcbio/pipeline/alignment.py | align_to_sort_bam | def align_to_sort_bam(fastq1, fastq2, aligner, data):
"""Align to the named genome build, returning a sorted BAM file.
"""
names = data["rgnames"]
align_dir_parts = [data["dirs"]["work"], "align", names["sample"]]
if data.get("disambiguate"):
align_dir_parts.append(data["disambiguate"]["geno... | python | def align_to_sort_bam(fastq1, fastq2, aligner, data):
"""Align to the named genome build, returning a sorted BAM file.
"""
names = data["rgnames"]
align_dir_parts = [data["dirs"]["work"], "align", names["sample"]]
if data.get("disambiguate"):
align_dir_parts.append(data["disambiguate"]["geno... | [
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224,227 | bcbio/bcbio-nextgen | bcbio/pipeline/alignment.py | get_aligner_with_aliases | def get_aligner_with_aliases(aligner, data):
"""Retrieve aligner index retriever, including aliases for shared.
Handles tricky cases like gridss where we need bwa indices even with
no aligner specified since they're used internally within GRIDSS.
"""
aligner_aliases = {"sentieon-bwa": "bwa"}
fr... | python | def get_aligner_with_aliases(aligner, data):
"""Retrieve aligner index retriever, including aliases for shared.
Handles tricky cases like gridss where we need bwa indices even with
no aligner specified since they're used internally within GRIDSS.
"""
aligner_aliases = {"sentieon-bwa": "bwa"}
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Handles tricky cases like gridss where we need bwa indices even with
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224,228 | bcbio/bcbio-nextgen | bcbio/pipeline/alignment.py | _get_aligner_index | def _get_aligner_index(aligner, data):
"""Handle multiple specifications of aligner indexes, returning value to pass to aligner.
Original bcbio case -- a list of indices.
CWL case: a single file with secondaryFiles staged in the same directory.
"""
aligner_indexes = tz.get_in(("reference", get_alig... | python | def _get_aligner_index(aligner, data):
"""Handle multiple specifications of aligner indexes, returning value to pass to aligner.
Original bcbio case -- a list of indices.
CWL case: a single file with secondaryFiles staged in the same directory.
"""
aligner_indexes = tz.get_in(("reference", get_alig... | [
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224,229 | bcbio/bcbio-nextgen | bcbio/pipeline/alignment.py | _align_from_fastq | def _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names,
align_dir, data):
"""Align from fastq inputs, producing sorted BAM output.
"""
config = data["config"]
align_fn = TOOLS[aligner].align_fn
out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
... | python | def _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names,
align_dir, data):
"""Align from fastq inputs, producing sorted BAM output.
"""
config = data["config"]
align_fn = TOOLS[aligner].align_fn
out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
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224,230 | bcbio/bcbio-nextgen | bcbio/structural/gridss.py | _finalize_memory | def _finalize_memory(jvm_opts):
"""GRIDSS does not recommend setting memory between 32 and 48Gb.
https://github.com/PapenfussLab/gridss#memory-usage
"""
avoid_min = 32
avoid_max = 48
out_opts = []
for opt in jvm_opts:
if opt.startswith("-Xmx"):
spec = opt[4:]
... | python | def _finalize_memory(jvm_opts):
"""GRIDSS does not recommend setting memory between 32 and 48Gb.
https://github.com/PapenfussLab/gridss#memory-usage
"""
avoid_min = 32
avoid_max = 48
out_opts = []
for opt in jvm_opts:
if opt.startswith("-Xmx"):
spec = opt[4:]
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224,231 | bcbio/bcbio-nextgen | bcbio/structural/gridss.py | _setup_reference_files | def _setup_reference_files(data, tx_out_dir):
"""Create a reference directory with fasta and bwa indices.
GRIDSS requires all files in a single directory, so setup with symlinks.
This needs bwa aligner indices available, which we ensure with `get_aligner_with_aliases`
during YAML sample setup.
"""
... | python | def _setup_reference_files(data, tx_out_dir):
"""Create a reference directory with fasta and bwa indices.
GRIDSS requires all files in a single directory, so setup with symlinks.
This needs bwa aligner indices available, which we ensure with `get_aligner_with_aliases`
during YAML sample setup.
"""
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224,232 | bcbio/bcbio-nextgen | bcbio/qc/multiqc.py | _add_versions | def _add_versions(samples):
"""Add tool and data versions to the summary.
"""
samples[0]["versions"] = {"tools": programs.write_versions(samples[0]["dirs"], samples[0]["config"]),
"data": provenancedata.write_versions(samples[0]["dirs"], samples)}
return samples | python | def _add_versions(samples):
"""Add tool and data versions to the summary.
"""
samples[0]["versions"] = {"tools": programs.write_versions(samples[0]["dirs"], samples[0]["config"]),
"data": provenancedata.write_versions(samples[0]["dirs"], samples)}
return samples | [
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224,233 | bcbio/bcbio-nextgen | bcbio/qc/multiqc.py | _summarize_inputs | def _summarize_inputs(samples, out_dir):
"""Summarize inputs for MultiQC reporting in display.
"""
logger.info("summarize target information")
if samples[0].get("analysis", "").lower() in ["variant", "variant2"]:
metrics_dir = utils.safe_makedir(os.path.join(out_dir, "report", "metrics"))
... | python | def _summarize_inputs(samples, out_dir):
"""Summarize inputs for MultiQC reporting in display.
"""
logger.info("summarize target information")
if samples[0].get("analysis", "").lower() in ["variant", "variant2"]:
metrics_dir = utils.safe_makedir(os.path.join(out_dir, "report", "metrics"))
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224,234 | bcbio/bcbio-nextgen | bcbio/qc/multiqc.py | _work_path_to_rel_final_path | def _work_path_to_rel_final_path(path, upload_path_mapping, upload_base_dir):
""" Check if `path` is a work-rooted path, and convert to a relative final-rooted path
"""
if not path or not isinstance(path, str):
return path
upload_path = None
# First, check in the mapping: if it's there is a... | python | def _work_path_to_rel_final_path(path, upload_path_mapping, upload_base_dir):
""" Check if `path` is a work-rooted path, and convert to a relative final-rooted path
"""
if not path or not isinstance(path, str):
return path
upload_path = None
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224,235 | bcbio/bcbio-nextgen | bcbio/qc/multiqc.py | _one_exists | def _one_exists(input_files):
"""
at least one file must exist for multiqc to run properly
"""
for f in input_files:
if os.path.exists(f):
return True
return False | python | def _one_exists(input_files):
"""
at least one file must exist for multiqc to run properly
"""
for f in input_files:
if os.path.exists(f):
return True
return False | [
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224,236 | bcbio/bcbio-nextgen | bcbio/qc/multiqc.py | _get_input_files | def _get_input_files(samples, base_dir, tx_out_dir):
"""Retrieve input files, keyed by sample and QC method name.
Stages files into the work directory to ensure correct names for
MultiQC sample assessment when running with CWL.
"""
in_files = collections.defaultdict(list)
for data in samples:
... | python | def _get_input_files(samples, base_dir, tx_out_dir):
"""Retrieve input files, keyed by sample and QC method name.
Stages files into the work directory to ensure correct names for
MultiQC sample assessment when running with CWL.
"""
in_files = collections.defaultdict(list)
for data in samples:
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224,237 | bcbio/bcbio-nextgen | bcbio/qc/multiqc.py | _group_by_sample_and_batch | def _group_by_sample_and_batch(samples):
"""Group samples split by QC method back one per sample-batch.
"""
out = collections.defaultdict(list)
for data in samples:
out[(dd.get_sample_name(data), dd.get_align_bam(data), tuple(_get_batches(data)))].append(data)
return [xs[0] for xs in out.val... | python | def _group_by_sample_and_batch(samples):
"""Group samples split by QC method back one per sample-batch.
"""
out = collections.defaultdict(list)
for data in samples:
out[(dd.get_sample_name(data), dd.get_align_bam(data), tuple(_get_batches(data)))].append(data)
return [xs[0] for xs in out.val... | [
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224,238 | bcbio/bcbio-nextgen | bcbio/qc/multiqc.py | _has_bcftools_germline_stats | def _has_bcftools_germline_stats(data):
"""Check for the presence of a germline stats file, CWL compatible.
"""
stats_file = tz.get_in(["summary", "qc"], data)
if isinstance(stats_file, dict):
stats_file = tz.get_in(["variants", "base"], stats_file)
if not stats_file:
stats_file = ""... | python | def _has_bcftools_germline_stats(data):
"""Check for the presence of a germline stats file, CWL compatible.
"""
stats_file = tz.get_in(["summary", "qc"], data)
if isinstance(stats_file, dict):
stats_file = tz.get_in(["variants", "base"], stats_file)
if not stats_file:
stats_file = ""... | [
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224,239 | bcbio/bcbio-nextgen | bcbio/qc/multiqc.py | _is_good_file_for_multiqc | def _is_good_file_for_multiqc(fpath):
"""Returns False if the file is binary or image."""
# Use mimetypes to exclude binary files where possible
(ftype, encoding) = mimetypes.guess_type(fpath)
if encoding is not None:
return False
if ftype is not None and ftype.startswith('image'):
r... | python | def _is_good_file_for_multiqc(fpath):
"""Returns False if the file is binary or image."""
# Use mimetypes to exclude binary files where possible
(ftype, encoding) = mimetypes.guess_type(fpath)
if encoding is not None:
return False
if ftype is not None and ftype.startswith('image'):
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224,240 | bcbio/bcbio-nextgen | bcbio/qc/multiqc.py | _parse_disambiguate | def _parse_disambiguate(disambiguatestatsfilename):
"""Parse disambiguation stats from given file.
"""
disambig_stats = [0, 0, 0]
with open(disambiguatestatsfilename, "r") as in_handle:
for i, line in enumerate(in_handle):
fields = line.strip().split("\t")
if i == 0:
... | python | def _parse_disambiguate(disambiguatestatsfilename):
"""Parse disambiguation stats from given file.
"""
disambig_stats = [0, 0, 0]
with open(disambiguatestatsfilename, "r") as in_handle:
for i, line in enumerate(in_handle):
fields = line.strip().split("\t")
if i == 0:
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224,241 | bcbio/bcbio-nextgen | bcbio/qc/multiqc.py | _merge_metrics | def _merge_metrics(samples, out_dir):
"""Merge metrics from multiple QC steps
"""
logger.info("summarize metrics")
out_dir = utils.safe_makedir(os.path.join(out_dir, "report", "metrics"))
sample_metrics = collections.defaultdict(dict)
for s in samples:
s = _add_disambiguate(s)
m ... | python | def _merge_metrics(samples, out_dir):
"""Merge metrics from multiple QC steps
"""
logger.info("summarize metrics")
out_dir = utils.safe_makedir(os.path.join(out_dir, "report", "metrics"))
sample_metrics = collections.defaultdict(dict)
for s in samples:
s = _add_disambiguate(s)
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/qc/multiqc.py#L456-L484 |
224,242 | bcbio/bcbio-nextgen | bcbio/qc/multiqc.py | _merge_fastqc | def _merge_fastqc(samples):
"""
merge all fastqc samples into one by module
"""
fastqc_list = collections.defaultdict(list)
seen = set()
for data in samples:
name = dd.get_sample_name(data)
if name in seen:
continue
seen.add(name)
fns = glob.glob(os.pa... | python | def _merge_fastqc(samples):
"""
merge all fastqc samples into one by module
"""
fastqc_list = collections.defaultdict(list)
seen = set()
for data in samples:
name = dd.get_sample_name(data)
if name in seen:
continue
seen.add(name)
fns = glob.glob(os.pa... | [
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224,243 | bcbio/bcbio-nextgen | scripts/utils/hla_loh_comparison.py | _create_plot | def _create_plot(tumor, in_glob, out_ext, page=1):
"""Create an output plot for the given PDF in the images directory.
"""
out_dir = utils.safe_makedir("images")
out_name = os.path.join(out_dir, "%s-%s" % (tumor, out_ext))
in_file = glob.glob(in_glob)[0]
cmd = ["pdftoppm", in_file, out_name, "-p... | python | def _create_plot(tumor, in_glob, out_ext, page=1):
"""Create an output plot for the given PDF in the images directory.
"""
out_dir = utils.safe_makedir("images")
out_name = os.path.join(out_dir, "%s-%s" % (tumor, out_ext))
in_file = glob.glob(in_glob)[0]
cmd = ["pdftoppm", in_file, out_name, "-p... | [
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224,244 | bcbio/bcbio-nextgen | scripts/utils/hla_loh_comparison.py | _get_cromwell_execution_dir | def _get_cromwell_execution_dir(base_dir, target_glob):
"""Retrieve the baseline directory with cromwell output files.
Handles Cromwell restarts where there are multiple work directories and
we traverse symlinks back to the original.
"""
cur_dir = glob.glob(os.path.join(base_dir, target_glob))[0]
... | python | def _get_cromwell_execution_dir(base_dir, target_glob):
"""Retrieve the baseline directory with cromwell output files.
Handles Cromwell restarts where there are multiple work directories and
we traverse symlinks back to the original.
"""
cur_dir = glob.glob(os.path.join(base_dir, target_glob))[0]
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224,245 | bcbio/bcbio-nextgen | scripts/utils/hla_loh_comparison.py | prep_bam_inputs | def prep_bam_inputs(out_dir, sample, call_file, bam_file):
"""Prepare expected input BAM files from pre-aligned.
"""
base = utils.splitext_plus(os.path.basename(bam_file))[0]
with open(call_file) as in_handle:
for cur_hla in (x.strip() for x in in_handle):
out_file = os.path.join(uti... | python | def prep_bam_inputs(out_dir, sample, call_file, bam_file):
"""Prepare expected input BAM files from pre-aligned.
"""
base = utils.splitext_plus(os.path.basename(bam_file))[0]
with open(call_file) as in_handle:
for cur_hla in (x.strip() for x in in_handle):
out_file = os.path.join(uti... | [
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224,246 | bcbio/bcbio-nextgen | scripts/utils/hla_loh_comparison.py | get_hla | def get_hla(sample, cromwell_dir, hla_glob):
"""Retrieve HLA calls and input fastqs for a sample.
"""
hla_dir = glob.glob(os.path.join(cromwell_dir, hla_glob, "align", sample, "hla"))[0]
fastq = os.path.join(hla_dir, "OptiType-HLA-A_B_C-input.fq")
calls = os.path.join(hla_dir, "%s-optitype.csv" % sa... | python | def get_hla(sample, cromwell_dir, hla_glob):
"""Retrieve HLA calls and input fastqs for a sample.
"""
hla_dir = glob.glob(os.path.join(cromwell_dir, hla_glob, "align", sample, "hla"))[0]
fastq = os.path.join(hla_dir, "OptiType-HLA-A_B_C-input.fq")
calls = os.path.join(hla_dir, "%s-optitype.csv" % sa... | [
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224,247 | bcbio/bcbio-nextgen | scripts/utils/hla_loh_comparison.py | name_to_absolute | def name_to_absolute(x):
"""Convert standard hg38 HLA name into ABSOLUTE naming.
"""
for c in ["-", "*", ":"]:
x = x.replace(c, "_")
x = x.lower()
return x | python | def name_to_absolute(x):
"""Convert standard hg38 HLA name into ABSOLUTE naming.
"""
for c in ["-", "*", ":"]:
x = x.replace(c, "_")
x = x.lower()
return x | [
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224,248 | bcbio/bcbio-nextgen | scripts/utils/hla_loh_comparison.py | get_hla_choice | def get_hla_choice(h, hlas, normal_bam, tumor_bam):
"""Retrieve matching HLA with best read support in both tumor and normal
"""
def get_counts(bam_file):
counts = {}
for line in subprocess.check_output(["samtools", "idxstats", bam_file]).split("\n"):
if line.startswith(h):
... | python | def get_hla_choice(h, hlas, normal_bam, tumor_bam):
"""Retrieve matching HLA with best read support in both tumor and normal
"""
def get_counts(bam_file):
counts = {}
for line in subprocess.check_output(["samtools", "idxstats", bam_file]).split("\n"):
if line.startswith(h):
... | [
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224,249 | bcbio/bcbio-nextgen | scripts/utils/hla_loh_comparison.py | prep_hla | def prep_hla(work_dir, sample, calls, hlas, normal_bam, tumor_bam):
"""Convert HLAs into ABSOLUTE format for use with LOHHLA.
LOHHLA hard codes names to hla_a, hla_b, hla_c so need to move
"""
work_dir = utils.safe_makedir(os.path.join(work_dir, sample, "inputs"))
hla_file = os.path.join(work_dir, ... | python | def prep_hla(work_dir, sample, calls, hlas, normal_bam, tumor_bam):
"""Convert HLAs into ABSOLUTE format for use with LOHHLA.
LOHHLA hard codes names to hla_a, hla_b, hla_c so need to move
"""
work_dir = utils.safe_makedir(os.path.join(work_dir, sample, "inputs"))
hla_file = os.path.join(work_dir, ... | [
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224,250 | bcbio/bcbio-nextgen | scripts/utils/hla_loh_comparison.py | prep_ploidy | def prep_ploidy(work_dir, sample, bam_file, cromwell_dir, sv_glob):
"""Create LOHHLA compatible input ploidy file from PureCN output.
"""
purecn_file = _get_cromwell_file(cromwell_dir, sv_glob, dict(sample=sample, method="purecn", ext="purecn.csv"))
work_dir = utils.safe_makedir(os.path.join(work_dir, s... | python | def prep_ploidy(work_dir, sample, bam_file, cromwell_dir, sv_glob):
"""Create LOHHLA compatible input ploidy file from PureCN output.
"""
purecn_file = _get_cromwell_file(cromwell_dir, sv_glob, dict(sample=sample, method="purecn", ext="purecn.csv"))
work_dir = utils.safe_makedir(os.path.join(work_dir, s... | [
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224,251 | bcbio/bcbio-nextgen | bcbio/ngsalign/bowtie.py | _bowtie_args_from_config | def _bowtie_args_from_config(data):
"""Configurable high level options for bowtie.
"""
config = data['config']
qual_format = config["algorithm"].get("quality_format", "")
if qual_format.lower() == "illumina":
qual_flags = ["--phred64-quals"]
else:
qual_flags = []
multi_mapper... | python | def _bowtie_args_from_config(data):
"""Configurable high level options for bowtie.
"""
config = data['config']
qual_format = config["algorithm"].get("quality_format", "")
if qual_format.lower() == "illumina":
qual_flags = ["--phred64-quals"]
else:
qual_flags = []
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224,252 | bcbio/bcbio-nextgen | bcbio/ngsalign/bowtie.py | align | def align(fastq_file, pair_file, ref_file, names, align_dir, data,
extra_args=None):
"""Do standard or paired end alignment with bowtie.
"""
num_hits = 1
if data["analysis"].lower().startswith("smallrna-seq"):
num_hits = 1000
config = data['config']
out_file = os.path.join(alig... | python | def align(fastq_file, pair_file, ref_file, names, align_dir, data,
extra_args=None):
"""Do standard or paired end alignment with bowtie.
"""
num_hits = 1
if data["analysis"].lower().startswith("smallrna-seq"):
num_hits = 1000
config = data['config']
out_file = os.path.join(alig... | [
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224,253 | bcbio/bcbio-nextgen | bcbio/heterogeneity/theta.py | subset_by_supported | def subset_by_supported(input_file, get_coords, calls_by_name, work_dir, data,
headers=("#",)):
"""Limit CNVkit input to calls with support from another caller.
get_coords is a function that return chrom, start, end from a line of the
input_file, allowing handling of multiple input ... | python | def subset_by_supported(input_file, get_coords, calls_by_name, work_dir, data,
headers=("#",)):
"""Limit CNVkit input to calls with support from another caller.
get_coords is a function that return chrom, start, end from a line of the
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224,254 | bcbio/bcbio-nextgen | bcbio/heterogeneity/theta.py | _input_to_bed | def _input_to_bed(theta_input, work_dir, get_coords, headers):
"""Convert input file to a BED file for comparisons
"""
theta_bed = os.path.join(work_dir, "%s.bed" % os.path.splitext(os.path.basename(theta_input))[0])
with open(theta_input) as in_handle:
with open(theta_bed, "w") as out_handle:
... | python | def _input_to_bed(theta_input, work_dir, get_coords, headers):
"""Convert input file to a BED file for comparisons
"""
theta_bed = os.path.join(work_dir, "%s.bed" % os.path.splitext(os.path.basename(theta_input))[0])
with open(theta_input) as in_handle:
with open(theta_bed, "w") as out_handle:
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224,255 | bcbio/bcbio-nextgen | bcbio/heterogeneity/theta.py | _run_theta | def _run_theta(cnv_info, data, work_dir, run_n3=True):
"""Run theta, calculating subpopulations and normal contamination.
"""
out = {"caller": "theta"}
max_normal = "0.9"
opts = ["-m", max_normal]
n2_result = _safe_run_theta(cnv_info["theta_input"], os.path.join(work_dir, "n2"), ".n2.results",
... | python | def _run_theta(cnv_info, data, work_dir, run_n3=True):
"""Run theta, calculating subpopulations and normal contamination.
"""
out = {"caller": "theta"}
max_normal = "0.9"
opts = ["-m", max_normal]
n2_result = _safe_run_theta(cnv_info["theta_input"], os.path.join(work_dir, "n2"), ".n2.results",
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224,256 | bcbio/bcbio-nextgen | bcbio/heterogeneity/theta.py | _update_with_calls | def _update_with_calls(result_file, cnv_file):
"""Update bounds with calls from CNVkit, inferred copy numbers and p-values from THetA.
"""
results = {}
with open(result_file) as in_handle:
in_handle.readline() # header
_, _, cs, ps = in_handle.readline().strip().split()
for i, (... | python | def _update_with_calls(result_file, cnv_file):
"""Update bounds with calls from CNVkit, inferred copy numbers and p-values from THetA.
"""
results = {}
with open(result_file) as in_handle:
in_handle.readline() # header
_, _, cs, ps = in_handle.readline().strip().split()
for i, (... | [
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224,257 | bcbio/bcbio-nextgen | bcbio/heterogeneity/theta.py | _merge_theta_calls | def _merge_theta_calls(bounds_file, result_file, cnv_file, data):
"""Create a final output file with merged CNVkit and THetA copy and population estimates.
"""
out_file = "%s-merged.txt" % (result_file.replace(".BEST.results", ""))
if not utils.file_uptodate(out_file, result_file):
with file_tra... | python | def _merge_theta_calls(bounds_file, result_file, cnv_file, data):
"""Create a final output file with merged CNVkit and THetA copy and population estimates.
"""
out_file = "%s-merged.txt" % (result_file.replace(".BEST.results", ""))
if not utils.file_uptodate(out_file, result_file):
with file_tra... | [
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224,258 | bcbio/bcbio-nextgen | bcbio/heterogeneity/theta.py | _select_model | def _select_model(n2_bounds, n2_result, n3_result, out_dir, data):
"""Run final model selection from n=2 and n=3 options.
"""
n2_out_file = n2_result.replace(".n2.results", ".BEST.results")
n3_out_file = n3_result.replace(".n3.results", ".BEST.results")
if not utils.file_exists(n2_out_file) and not ... | python | def _select_model(n2_bounds, n2_result, n3_result, out_dir, data):
"""Run final model selection from n=2 and n=3 options.
"""
n2_out_file = n2_result.replace(".n2.results", ".BEST.results")
n3_out_file = n3_result.replace(".n3.results", ".BEST.results")
if not utils.file_exists(n2_out_file) and not ... | [
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224,259 | bcbio/bcbio-nextgen | bcbio/heterogeneity/theta.py | _safe_run_theta | def _safe_run_theta(input_file, out_dir, output_ext, args, data):
"""Run THetA, catching and continuing on any errors.
"""
out_file = os.path.join(out_dir, _split_theta_ext(input_file) + output_ext)
skip_file = out_file + ".skipped"
if utils.file_exists(skip_file):
return None
if not uti... | python | def _safe_run_theta(input_file, out_dir, output_ext, args, data):
"""Run THetA, catching and continuing on any errors.
"""
out_file = os.path.join(out_dir, _split_theta_ext(input_file) + output_ext)
skip_file = out_file + ".skipped"
if utils.file_exists(skip_file):
return None
if not uti... | [
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224,260 | bcbio/bcbio-nextgen | bcbio/heterogeneity/theta.py | _get_cmd | def _get_cmd(cmd):
"""Retrieve required commands for running THetA with our local bcbio python.
"""
check_cmd = "RunTHetA.py"
try:
local_cmd = subprocess.check_output(["which", check_cmd]).strip()
except subprocess.CalledProcessError:
return None
return [sys.executable, "%s/%s" %... | python | def _get_cmd(cmd):
"""Retrieve required commands for running THetA with our local bcbio python.
"""
check_cmd = "RunTHetA.py"
try:
local_cmd = subprocess.check_output(["which", check_cmd]).strip()
except subprocess.CalledProcessError:
return None
return [sys.executable, "%s/%s" %... | [
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224,261 | bcbio/bcbio-nextgen | bcbio/srna/mirge.py | run | def run(data):
"""Proxy function to run the tool"""
sample = data[0][0]
work_dir = dd.get_work_dir(sample)
out_dir = os.path.join(work_dir, "mirge")
lib = _find_lib(sample)
mirge = _find_mirge(sample)
bowtie = _find_bowtie(sample)
sps = dd.get_species(sample)
species = SPS.get(sps, "... | python | def run(data):
"""Proxy function to run the tool"""
sample = data[0][0]
work_dir = dd.get_work_dir(sample)
out_dir = os.path.join(work_dir, "mirge")
lib = _find_lib(sample)
mirge = _find_mirge(sample)
bowtie = _find_bowtie(sample)
sps = dd.get_species(sample)
species = SPS.get(sps, "... | [
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224,262 | bcbio/bcbio-nextgen | bcbio/srna/mirge.py | _create_sample_file | def _create_sample_file(data, out_dir):
"""from data list all the fastq files in a file"""
sample_file = os.path.join(out_dir, "sample_file.txt")
with open(sample_file, 'w') as outh:
for sample in data:
outh.write(sample[0]["clean_fastq"] + "\n")
return sample_file | python | def _create_sample_file(data, out_dir):
"""from data list all the fastq files in a file"""
sample_file = os.path.join(out_dir, "sample_file.txt")
with open(sample_file, 'w') as outh:
for sample in data:
outh.write(sample[0]["clean_fastq"] + "\n")
return sample_file | [
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224,263 | bcbio/bcbio-nextgen | bcbio/srna/mirge.py | _find_lib | def _find_lib(data):
"""Find mirge libs"""
options = " ".join(data.get('resources', {}).get('mirge', {}).get("options", ""))
if options.find("-lib") > -1 and utils.file_exists(options.split()[1]):
return options
if not options:
logger.warning("miRge libraries not found. Follow these inst... | python | def _find_lib(data):
"""Find mirge libs"""
options = " ".join(data.get('resources', {}).get('mirge', {}).get("options", ""))
if options.find("-lib") > -1 and utils.file_exists(options.split()[1]):
return options
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224,264 | bcbio/bcbio-nextgen | bcbio/pipeline/datadict.py | get_input_sequence_files | def get_input_sequence_files(data, default=None):
"""
returns the input sequencing files, these can be single or paired FASTQ
files or BAM files
"""
if "files" not in data or data.get("files") is None:
file1, file2 = None, None
elif len(data["files"]) == 2:
file1, file2 = data["f... | python | def get_input_sequence_files(data, default=None):
"""
returns the input sequencing files, these can be single or paired FASTQ
files or BAM files
"""
if "files" not in data or data.get("files") is None:
file1, file2 = None, None
elif len(data["files"]) == 2:
file1, file2 = data["f... | [
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224,265 | bcbio/bcbio-nextgen | bcbio/pipeline/datadict.py | get_umi_consensus | def get_umi_consensus(data):
"""Retrieve UMI for consensus based preparation.
We specify this either as a separate fastq file or embedded
in the read name as `fastq_name`.`
"""
consensus_choices = (["fastq_name"])
umi = tz.get_in(["config", "algorithm", "umi_type"], data)
# don't run consen... | python | def get_umi_consensus(data):
"""Retrieve UMI for consensus based preparation.
We specify this either as a separate fastq file or embedded
in the read name as `fastq_name`.`
"""
consensus_choices = (["fastq_name"])
umi = tz.get_in(["config", "algorithm", "umi_type"], data)
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224,266 | bcbio/bcbio-nextgen | bcbio/pipeline/datadict.py | get_dexseq_gff | def get_dexseq_gff(config, default=None):
"""
some older versions of the genomes have the DEXseq gff file as
gff instead of gff3, so this handles that by looking for either one
"""
dexseq_gff = tz.get_in(tz.get_in(['dexseq_gff', 'keys'], LOOKUPS, {}),
config, None)
if ... | python | def get_dexseq_gff(config, default=None):
"""
some older versions of the genomes have the DEXseq gff file as
gff instead of gff3, so this handles that by looking for either one
"""
dexseq_gff = tz.get_in(tz.get_in(['dexseq_gff', 'keys'], LOOKUPS, {}),
config, None)
if ... | [
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224,267 | bcbio/bcbio-nextgen | bcbio/pipeline/datadict.py | get_in_samples | def get_in_samples(samples, fn):
"""
for a list of samples, return the value of a global option
"""
for sample in samples:
sample = to_single_data(sample)
if fn(sample, None):
return fn(sample)
return None | python | def get_in_samples(samples, fn):
"""
for a list of samples, return the value of a global option
"""
for sample in samples:
sample = to_single_data(sample)
if fn(sample, None):
return fn(sample)
return None | [
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224,268 | bcbio/bcbio-nextgen | bcbio/pipeline/datadict.py | update_summary_qc | def update_summary_qc(data, key, base=None, secondary=None):
"""
updates summary_qc with a new section, keyed by key.
stick files into summary_qc if you want them propagated forward
and available for multiqc
"""
summary = get_summary_qc(data, {})
if base and secondary:
summary[key] =... | python | def update_summary_qc(data, key, base=None, secondary=None):
"""
updates summary_qc with a new section, keyed by key.
stick files into summary_qc if you want them propagated forward
and available for multiqc
"""
summary = get_summary_qc(data, {})
if base and secondary:
summary[key] =... | [
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224,269 | bcbio/bcbio-nextgen | bcbio/pipeline/datadict.py | has_variantcalls | def has_variantcalls(data):
"""
returns True if the data dictionary is configured for variant calling
"""
analysis = get_analysis(data).lower()
variant_pipeline = analysis.startswith(("standard", "variant", "variant2"))
variantcaller = get_variantcaller(data)
return variant_pipeline or varia... | python | def has_variantcalls(data):
"""
returns True if the data dictionary is configured for variant calling
"""
analysis = get_analysis(data).lower()
variant_pipeline = analysis.startswith(("standard", "variant", "variant2"))
variantcaller = get_variantcaller(data)
return variant_pipeline or varia... | [
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224,270 | bcbio/bcbio-nextgen | bcbio/rnaseq/qc.py | estimate_library_complexity | def estimate_library_complexity(df, algorithm="RNA-seq"):
"""
estimate library complexity from the number of reads vs.
number of unique start sites. returns "NA" if there are
not enough data points to fit the line
"""
DEFAULT_CUTOFFS = {"RNA-seq": (0.25, 0.40)}
cutoffs = DEFAULT_CUTOFFS[algo... | python | def estimate_library_complexity(df, algorithm="RNA-seq"):
"""
estimate library complexity from the number of reads vs.
number of unique start sites. returns "NA" if there are
not enough data points to fit the line
"""
DEFAULT_CUTOFFS = {"RNA-seq": (0.25, 0.40)}
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224,271 | bcbio/bcbio-nextgen | bcbio/galaxy/api.py | GalaxyApiAccess.run_details | def run_details(self, run_bc, run_date=None):
"""Next Gen LIMS specific API functionality.
"""
try:
details = self._get("/nglims/api_run_details", dict(run=run_bc))
except ValueError:
raise ValueError("Could not find information in Galaxy for run: %s" % run_bc)
... | python | def run_details(self, run_bc, run_date=None):
"""Next Gen LIMS specific API functionality.
"""
try:
details = self._get("/nglims/api_run_details", dict(run=run_bc))
except ValueError:
raise ValueError("Could not find information in Galaxy for run: %s" % run_bc)
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224,272 | bcbio/bcbio-nextgen | bcbio/pipeline/cleanbam.py | fixrg | def fixrg(in_bam, names, ref_file, dirs, data):
"""Fix read group in a file, using samtools addreplacerg.
addreplacerg does not remove the old read group, causing confusion when
checking. We use reheader to work around this
"""
work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "bamc... | python | def fixrg(in_bam, names, ref_file, dirs, data):
"""Fix read group in a file, using samtools addreplacerg.
addreplacerg does not remove the old read group, causing confusion when
checking. We use reheader to work around this
"""
work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "bamc... | [
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224,273 | bcbio/bcbio-nextgen | bcbio/pipeline/cleanbam.py | _target_chroms_and_header | def _target_chroms_and_header(bam_file, data):
"""Get a list of chromosomes to target and new updated ref_file header.
Could potentially handle remapping from chr1 -> 1 but currently disabled due
to speed issues.
"""
special_remaps = {"chrM": "MT", "MT": "chrM"}
target_chroms = dict([(x.name, i... | python | def _target_chroms_and_header(bam_file, data):
"""Get a list of chromosomes to target and new updated ref_file header.
Could potentially handle remapping from chr1 -> 1 but currently disabled due
to speed issues.
"""
special_remaps = {"chrM": "MT", "MT": "chrM"}
target_chroms = dict([(x.name, i... | [
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224,274 | bcbio/bcbio-nextgen | bcbio/pipeline/cleanbam.py | picard_prep | def picard_prep(in_bam, names, ref_file, dirs, data):
"""Prepare input BAM using Picard and GATK cleaning tools.
- ReorderSam to reorder file to reference
- AddOrReplaceReadGroups to add read group information and coordinate sort
- PrintReads to filters to remove problem records:
- filterMBQ to rem... | python | def picard_prep(in_bam, names, ref_file, dirs, data):
"""Prepare input BAM using Picard and GATK cleaning tools.
- ReorderSam to reorder file to reference
- AddOrReplaceReadGroups to add read group information and coordinate sort
- PrintReads to filters to remove problem records:
- filterMBQ to rem... | [
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224,275 | bcbio/bcbio-nextgen | bcbio/pipeline/cleanbam.py | _filter_bad_reads | def _filter_bad_reads(in_bam, ref_file, data):
"""Use GATK filter to remove problem reads which choke GATK and Picard.
"""
bam.index(in_bam, data["config"])
out_file = "%s-gatkfilter.bam" % os.path.splitext(in_bam)[0]
if not utils.file_exists(out_file):
with tx_tmpdir(data) as tmp_dir:
... | python | def _filter_bad_reads(in_bam, ref_file, data):
"""Use GATK filter to remove problem reads which choke GATK and Picard.
"""
bam.index(in_bam, data["config"])
out_file = "%s-gatkfilter.bam" % os.path.splitext(in_bam)[0]
if not utils.file_exists(out_file):
with tx_tmpdir(data) as tmp_dir:
... | [
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224,276 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | generate_parallel | def generate_parallel(samples, run_parallel):
"""Provide parallel preparation of summary information for alignment and variant calling.
"""
to_analyze, extras = _split_samples_by_qc(samples)
qced = run_parallel("pipeline_summary", to_analyze)
samples = _combine_qc_samples(qced) + extras
qsign_in... | python | def generate_parallel(samples, run_parallel):
"""Provide parallel preparation of summary information for alignment and variant calling.
"""
to_analyze, extras = _split_samples_by_qc(samples)
qced = run_parallel("pipeline_summary", to_analyze)
samples = _combine_qc_samples(qced) + extras
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224,277 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | pipeline_summary | def pipeline_summary(data):
"""Provide summary information on processing sample.
Handles standard and CWL (single QC output) cases.
"""
data = utils.to_single_data(data)
work_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
if not work_bam or not work_bam.endswith(".bam"):
work_bam... | python | def pipeline_summary(data):
"""Provide summary information on processing sample.
Handles standard and CWL (single QC output) cases.
"""
data = utils.to_single_data(data)
work_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
if not work_bam or not work_bam.endswith(".bam"):
work_bam... | [
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224,278 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | get_qc_tools | def get_qc_tools(data):
"""Retrieve a list of QC tools to use based on configuration and analysis type.
Uses defaults if previously set.
"""
if dd.get_algorithm_qc(data):
return dd.get_algorithm_qc(data)
analysis = data["analysis"].lower()
to_run = []
if tz.get_in(["config", "algori... | python | def get_qc_tools(data):
"""Retrieve a list of QC tools to use based on configuration and analysis type.
Uses defaults if previously set.
"""
if dd.get_algorithm_qc(data):
return dd.get_algorithm_qc(data)
analysis = data["analysis"].lower()
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224,279 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | _run_qc_tools | def _run_qc_tools(bam_file, data):
"""Run a set of third party quality control tools, returning QC directory and metrics.
:param bam_file: alignments in bam format
:param data: dict with all configuration information
:returns: dict with output of different tools
"""
from bcbio.qc i... | python | def _run_qc_tools(bam_file, data):
"""Run a set of third party quality control tools, returning QC directory and metrics.
:param bam_file: alignments in bam format
:param data: dict with all configuration information
:returns: dict with output of different tools
"""
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224,280 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | _organize_qc_files | def _organize_qc_files(program, qc_dir):
"""Organize outputs from quality control runs into a base file and secondary outputs.
Provides compatibility with CWL output. Returns None if no files created during processing.
"""
base_files = {"fastqc": "fastqc_report.html",
"qualimap_rnaseq... | python | def _organize_qc_files(program, qc_dir):
"""Organize outputs from quality control runs into a base file and secondary outputs.
Provides compatibility with CWL output. Returns None if no files created during processing.
"""
base_files = {"fastqc": "fastqc_report.html",
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224,281 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | _split_samples_by_qc | def _split_samples_by_qc(samples):
"""Split data into individual quality control steps for a run.
"""
to_process = []
extras = []
for data in [utils.to_single_data(x) for x in samples]:
qcs = dd.get_algorithm_qc(data)
# kraken doesn't need bam
if qcs and (dd.get_align_bam(dat... | python | def _split_samples_by_qc(samples):
"""Split data into individual quality control steps for a run.
"""
to_process = []
extras = []
for data in [utils.to_single_data(x) for x in samples]:
qcs = dd.get_algorithm_qc(data)
# kraken doesn't need bam
if qcs and (dd.get_align_bam(dat... | [
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224,282 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | _combine_qc_samples | def _combine_qc_samples(samples):
"""Combine split QC analyses into single samples based on BAM files.
"""
by_bam = collections.defaultdict(list)
for data in [utils.to_single_data(x) for x in samples]:
batch = dd.get_batch(data) or dd.get_sample_name(data)
if not isinstance(batch, (list,... | python | def _combine_qc_samples(samples):
"""Combine split QC analyses into single samples based on BAM files.
"""
by_bam = collections.defaultdict(list)
for data in [utils.to_single_data(x) for x in samples]:
batch = dd.get_batch(data) or dd.get_sample_name(data)
if not isinstance(batch, (list,... | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/pipeline/qcsummary.py#L242-L266 |
224,283 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | write_project_summary | def write_project_summary(samples, qsign_info=None):
"""Write project summary information on the provided samples.
write out dirs, genome resources,
"""
work_dir = samples[0][0]["dirs"]["work"]
out_file = os.path.join(work_dir, "project-summary.yaml")
upload_dir = (os.path.join(work_dir, sample... | python | def write_project_summary(samples, qsign_info=None):
"""Write project summary information on the provided samples.
write out dirs, genome resources,
"""
work_dir = samples[0][0]["dirs"]["work"]
out_file = os.path.join(work_dir, "project-summary.yaml")
upload_dir = (os.path.join(work_dir, sample... | [
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224,284 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | _merge_metadata | def _merge_metadata(samples):
"""Merge all metadata into CSV file"""
samples = list(utils.flatten(samples))
out_dir = dd.get_work_dir(samples[0])
logger.info("summarize metadata")
out_file = os.path.join(out_dir, "metadata.csv")
sample_metrics = collections.defaultdict(dict)
for s in samples... | python | def _merge_metadata(samples):
"""Merge all metadata into CSV file"""
samples = list(utils.flatten(samples))
out_dir = dd.get_work_dir(samples[0])
logger.info("summarize metadata")
out_file = os.path.join(out_dir, "metadata.csv")
sample_metrics = collections.defaultdict(dict)
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224,285 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | _other_pipeline_samples | def _other_pipeline_samples(summary_file, cur_samples):
"""Retrieve samples produced previously by another pipeline in the summary output.
"""
cur_descriptions = set([s[0]["description"] for s in cur_samples])
out = []
if utils.file_exists(summary_file):
with open(summary_file) as in_handle:... | python | def _other_pipeline_samples(summary_file, cur_samples):
"""Retrieve samples produced previously by another pipeline in the summary output.
"""
cur_descriptions = set([s[0]["description"] for s in cur_samples])
out = []
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224,286 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | _add_researcher_summary | def _add_researcher_summary(samples, summary_yaml):
"""Generate summary files per researcher if organized via a LIMS.
"""
by_researcher = collections.defaultdict(list)
for data in (x[0] for x in samples):
researcher = utils.get_in(data, ("upload", "researcher"))
if researcher:
... | python | def _add_researcher_summary(samples, summary_yaml):
"""Generate summary files per researcher if organized via a LIMS.
"""
by_researcher = collections.defaultdict(list)
for data in (x[0] for x in samples):
researcher = utils.get_in(data, ("upload", "researcher"))
if researcher:
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224,287 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | _summary_csv_by_researcher | def _summary_csv_by_researcher(summary_yaml, researcher, descrs, data):
"""Generate a CSV file with summary information for a researcher on this project.
"""
out_file = os.path.join(utils.safe_makedir(os.path.join(data["dirs"]["work"], "researcher")),
"%s-summary.tsv" % run_info.... | python | def _summary_csv_by_researcher(summary_yaml, researcher, descrs, data):
"""Generate a CSV file with summary information for a researcher on this project.
"""
out_file = os.path.join(utils.safe_makedir(os.path.join(data["dirs"]["work"], "researcher")),
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224,288 | bcbio/bcbio-nextgen | bcbio/pipeline/qcsummary.py | prep_pdf | def prep_pdf(qc_dir, config):
"""Create PDF from HTML summary outputs in QC directory.
Requires wkhtmltopdf installed: http://www.msweet.org/projects.php?Z1
Thanks to: https://www.biostars.org/p/16991/
Works around issues with CSS conversion on CentOS by adjusting CSS.
"""
html_file = os.path.... | python | def prep_pdf(qc_dir, config):
"""Create PDF from HTML summary outputs in QC directory.
Requires wkhtmltopdf installed: http://www.msweet.org/projects.php?Z1
Thanks to: https://www.biostars.org/p/16991/
Works around issues with CSS conversion on CentOS by adjusting CSS.
"""
html_file = os.path.... | [
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224,289 | bcbio/bcbio-nextgen | bcbio/structural/purecn.py | _run_purecn_dx | def _run_purecn_dx(out, paired):
"""Extract signatures and mutational burdens from PureCN rds file.
"""
out_base, out, all_files = _get_purecn_dx_files(paired, out)
if not utils.file_uptodate(out["mutation_burden"], out["rds"]):
with file_transaction(paired.tumor_data, out_base) as tx_out_base:
... | python | def _run_purecn_dx(out, paired):
"""Extract signatures and mutational burdens from PureCN rds file.
"""
out_base, out, all_files = _get_purecn_dx_files(paired, out)
if not utils.file_uptodate(out["mutation_burden"], out["rds"]):
with file_transaction(paired.tumor_data, out_base) as tx_out_base:
... | [
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224,290 | bcbio/bcbio-nextgen | bcbio/structural/purecn.py | _get_purecn_dx_files | def _get_purecn_dx_files(paired, out):
"""Retrieve files generated by PureCN_Dx
"""
out_base = "%s-dx" % utils.splitext_plus(out["rds"])[0]
all_files = []
for key, ext in [[("mutation_burden",), "_mutation_burden.csv"],
[("plot", "signatures"), "_signatures.pdf"],
... | python | def _get_purecn_dx_files(paired, out):
"""Retrieve files generated by PureCN_Dx
"""
out_base = "%s-dx" % utils.splitext_plus(out["rds"])[0]
all_files = []
for key, ext in [[("mutation_burden",), "_mutation_burden.csv"],
[("plot", "signatures"), "_signatures.pdf"],
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224,291 | bcbio/bcbio-nextgen | bcbio/structural/purecn.py | _run_purecn | def _run_purecn(paired, work_dir):
"""Run PureCN.R wrapper with pre-segmented CNVkit or GATK4 inputs.
"""
segfns = {"cnvkit": _segment_normalized_cnvkit, "gatk-cnv": _segment_normalized_gatk}
out_base, out, all_files = _get_purecn_files(paired, work_dir)
failed_file = out_base + "-failed.log"
cn... | python | def _run_purecn(paired, work_dir):
"""Run PureCN.R wrapper with pre-segmented CNVkit or GATK4 inputs.
"""
segfns = {"cnvkit": _segment_normalized_cnvkit, "gatk-cnv": _segment_normalized_gatk}
out_base, out, all_files = _get_purecn_files(paired, work_dir)
failed_file = out_base + "-failed.log"
cn... | [
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224,292 | bcbio/bcbio-nextgen | bcbio/structural/purecn.py | _segment_normalized_gatk | def _segment_normalized_gatk(cnr_file, work_dir, paired):
"""Segmentation of normalized inputs using GATK4, converting into standard input formats.
"""
work_dir = utils.safe_makedir(os.path.join(work_dir, "gatk-cnv"))
seg_file = gatkcnv.model_segments(cnr_file, work_dir, paired)["seg"]
std_seg_file ... | python | def _segment_normalized_gatk(cnr_file, work_dir, paired):
"""Segmentation of normalized inputs using GATK4, converting into standard input formats.
"""
work_dir = utils.safe_makedir(os.path.join(work_dir, "gatk-cnv"))
seg_file = gatkcnv.model_segments(cnr_file, work_dir, paired)["seg"]
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224,293 | bcbio/bcbio-nextgen | bcbio/structural/purecn.py | _segment_normalized_cnvkit | def _segment_normalized_cnvkit(cnr_file, work_dir, paired):
"""Segmentation of normalized inputs using CNVkit.
"""
cnvkit_base = os.path.join(utils.safe_makedir(os.path.join(work_dir, "cnvkit")),
dd.get_sample_name(paired.tumor_data))
cnr_file = chromhacks.bed_to_standard... | python | def _segment_normalized_cnvkit(cnr_file, work_dir, paired):
"""Segmentation of normalized inputs using CNVkit.
"""
cnvkit_base = os.path.join(utils.safe_makedir(os.path.join(work_dir, "cnvkit")),
dd.get_sample_name(paired.tumor_data))
cnr_file = chromhacks.bed_to_standard... | [
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224,294 | bcbio/bcbio-nextgen | bcbio/structural/purecn.py | _remove_overlaps | def _remove_overlaps(in_file, out_dir, data):
"""Remove regions that overlap with next region, these result in issues with PureCN.
"""
out_file = os.path.join(out_dir, "%s-nooverlaps%s" % utils.splitext_plus(os.path.basename(in_file)))
if not utils.file_uptodate(out_file, in_file):
with file_tra... | python | def _remove_overlaps(in_file, out_dir, data):
"""Remove regions that overlap with next region, these result in issues with PureCN.
"""
out_file = os.path.join(out_dir, "%s-nooverlaps%s" % utils.splitext_plus(os.path.basename(in_file)))
if not utils.file_uptodate(out_file, in_file):
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224,295 | bcbio/bcbio-nextgen | bcbio/structural/purecn.py | _get_purecn_files | def _get_purecn_files(paired, work_dir, require_exist=False):
"""Retrieve organized structure of PureCN output files.
"""
out_base = os.path.join(work_dir, "%s-purecn" % (dd.get_sample_name(paired.tumor_data)))
out = {"plot": {}}
all_files = []
for plot in ["chromosomes", "local_optima", "segmen... | python | def _get_purecn_files(paired, work_dir, require_exist=False):
"""Retrieve organized structure of PureCN output files.
"""
out_base = os.path.join(work_dir, "%s-purecn" % (dd.get_sample_name(paired.tumor_data)))
out = {"plot": {}}
all_files = []
for plot in ["chromosomes", "local_optima", "segmen... | [
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224,296 | bcbio/bcbio-nextgen | bcbio/structural/purecn.py | _loh_to_vcf | def _loh_to_vcf(cur):
"""Convert LOH output into standardized VCF.
"""
cn = int(float(cur["C"]))
minor_cn = int(float(cur["M"]))
if cur["type"].find("LOH"):
svtype = "LOH"
elif cn > 2:
svtype = "DUP"
elif cn < 1:
svtype = "DEL"
else:
svtype = None
if s... | python | def _loh_to_vcf(cur):
"""Convert LOH output into standardized VCF.
"""
cn = int(float(cur["C"]))
minor_cn = int(float(cur["M"]))
if cur["type"].find("LOH"):
svtype = "LOH"
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svtype = "DUP"
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svtype = "DEL"
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svtype = None
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... | Convert LOH output into standardized VCF. | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/purecn.py#L219-L237 |
224,297 | bcbio/bcbio-nextgen | scripts/utils/collect_metrics_to_csv.py | _generate_metrics | def _generate_metrics(bam_fname, config_file, ref_file,
bait_file, target_file):
"""Run Picard commands to generate metrics files when missing.
"""
with open(config_file) as in_handle:
config = yaml.safe_load(in_handle)
broad_runner = broad.runner_from_config(config)
ba... | python | def _generate_metrics(bam_fname, config_file, ref_file,
bait_file, target_file):
"""Run Picard commands to generate metrics files when missing.
"""
with open(config_file) as in_handle:
config = yaml.safe_load(in_handle)
broad_runner = broad.runner_from_config(config)
ba... | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/scripts/utils/collect_metrics_to_csv.py#L135-L155 |
224,298 | bcbio/bcbio-nextgen | bcbio/structural/gatkcnv.py | run | def run(items, background=None):
"""Detect copy number variations from batched set of samples using GATK4 CNV calling.
TODO: implement germline calling with DetermineGermlineContigPloidy and GermlineCNVCaller
"""
if not background: background = []
paired = vcfutils.get_paired(items + background)
... | python | def run(items, background=None):
"""Detect copy number variations from batched set of samples using GATK4 CNV calling.
TODO: implement germline calling with DetermineGermlineContigPloidy and GermlineCNVCaller
"""
if not background: background = []
paired = vcfutils.get_paired(items + background)
... | [
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TODO: implement germline calling with DetermineGermlineContigPloidy and GermlineCNVCaller | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/gatkcnv.py#L19-L32 |
224,299 | bcbio/bcbio-nextgen | bcbio/structural/gatkcnv.py | _run_paired | def _run_paired(paired):
"""Run somatic variant calling pipeline.
"""
from bcbio.structural import titancna
work_dir = _sv_workdir(paired.tumor_data)
seg_files = model_segments(tz.get_in(["depth", "bins", "normalized"], paired.tumor_data),
work_dir, paired)
call_fi... | python | def _run_paired(paired):
"""Run somatic variant calling pipeline.
"""
from bcbio.structural import titancna
work_dir = _sv_workdir(paired.tumor_data)
seg_files = model_segments(tz.get_in(["depth", "bins", "normalized"], paired.tumor_data),
work_dir, paired)
call_fi... | [
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] | 6a9348c0054ccd5baffd22f1bb7d0422f6978b20 | https://github.com/bcbio/bcbio-nextgen/blob/6a9348c0054ccd5baffd22f1bb7d0422f6978b20/bcbio/structural/gatkcnv.py#L34-L54 |
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